fix ode-energy-sample and clean/fix librr stuff #361
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- introduce `update_time_step` in `RoadRunnerIntracellular`
- set for each instance of `RoadRunnerIntracellular`
- this controls the timestep for the model
- will be set to `intracellular_dt` if not specified in the xml for the given cell type
- add the `intracellular_dt` element as a child of the `intracellular` element in the xml
- could be set on a cell-by-cell basis if desired
- introduce `previous_update_time` in `RoadRunnerIntracellular`
- tracks the previous update time
- used to determine how long to run the ODE when updating
- set to `current_time` when copying/cloning
- fix `next_librr_run` in `RoadRunnerIntracellular`
- was not being updated and thus ODE models were running at every time step
- check `current_time >= next_librr_run - 0.5 * diffusion_dt` to determine if an update is needed
- cleaned up librr files
- fixed and cleand ode-energy-sample
- it was running the intracellular models in `main.cpp` and in the update cells function
- it seemed to try to set intracellular_dt inside the intracellular element of the xml
- messy custom.cpp and custom.h
before, only new ones were validated. those "copied" from previously read defs were not Presumably, it was assumed that they fully inherited their parent's model, but as of now, they read the xml to get their model, so they need to be validated.
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See PR #362 for a better update to the libRR api. |
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Update [25-02-13]: See PR #362 for a better update to the libRR api.
update_time_stepinRoadRunnerIntracellularRoadRunnerIntracellularintracellular_dtif not specified in the xml for the given cell typeintracellular_dtelement as a child of theintracellularelement in the xmlprevious_update_timeinRoadRunnerIntracellularcurrent_timewhen copying/cloningnext_librr_runinRoadRunnerIntracellularcurrent_time >= next_librr_run - 0.5 * diffusion_dtto determine if an update is neededcurrent_time + update_time_stepwhen copying/cloningmain.cppand in the update cells function